References
- Aamir, M., Singh, V. K., Meena, M., Upadhyay, R. S., Gupta, V. K., & Singh, S. (2017). structural and functional insights into WRKY3 and WRKY4 transcription factors to unravel the WRKY-DNA (W-Box) complex interaction in Tomato (Solanum lycopersicum L.). A computational approach. Frontiers in Plant Science, 8, 819. https://doi.org/https://doi.org/10.3389/fpls.2017.00819
- Arnold, K., Bordoli, L., Kopp, J., & Schwede, T. (2006). The SWISS-MODEL workspace: A web-based environment for protein structure homology modelling. Bioinformatics (Oxford, England), 22(2), 195–201. https://doi.org/https://doi.org/10.1093/bioinformatics/bti770
- Atkins, M., Jiang, Y., Sansores-Garcia, L., Jusiak, B., Halder, G., & Mardon, G. (2013). Dynamic rewiring of the Drosophila retinal determination network switches its function from selector to differentiation. PLoS Genetics, 9(8), e1003731https://doi.org/https://doi.org/10.1371/journal.pgen.1003731
- Benkert, P., Biasini, M., & Schwede, T. (2011). Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics (Oxford, England), 27(3), 343–350. https://doi.org/https://doi.org/10.1093/bioinformatics/btq662
- Boyartchuk, V. L., Ashby, M. N., & Rine, J. (1997). Modulation of Ras and a-factor function by carboxyl-terminal proteolysis. Science (New York, N.Y.), 275(5307), 1796–1800. https://doi.org/https://doi.org/10.1126/science.275.5307.1796
- Chen, K., Wu, K., Cai, S., Zhang, W., Zhou, J., Wang, J., Ertel, A., Li, Z., Rui, H., Quong, A., Lisanti, M. P., Tozeren, A., Tanes, C., Addya, S., Gormley, M., Wang, C., McMahon, S. B., & Pestell, R. G. (2013). Dachshund binds p53 to block the growth of lung adenocarcinoma cells. Cancer Research, 73(11), 3262–3274. https://doi.org/https://doi.org/10.1158/0008-5472.CAN-12-3191
- Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S., & Richardson, D. C. (2010). MolProbity: All-atom structure validation for macromolecular crystallography. Acta Crystallographica. Section D, Biological Crystallography, 66(Pt 1), 12–21. https://doi.org/https://doi.org/10.1107/S0907444909042073
- Chu, Q., Han, N., Yuan, X., Nie, X., Wu, H., Chen, Y., Guo, M., Yu, S., & Wu, K. (2014). DACH1 inhibits cyclin D1 expression, cellular proliferation and tumor growth of renal cancer cells. Journal of Hematology & Oncology, 7, 73https://doi.org/https://doi.org/10.1186/s13045-014-0073-5
- Dalgin, G. S., Drever, M., Williams, T., King, T., DeLisi, C., & Liou, L. S. (2008). Identification of novel epigenetic markers for clear cell renal cell carcinoma. The Journal of Urology, 180(3), 1126–1130. https://doi.org/https://doi.org/10.1016/j.juro.2008.04.137
- Ferreira, R. J., Ferreira, M. J., Daniel, U., & dos Santos, J. V. A. (2012). Insights on P-glycoprotein’s efflux mechanism obtained by molecular dynamics simulations. Journal of Chemical Theory and Computation, 8(6), 1853–1864. https://doi.org/https://doi.org/10.1021/ct300083m
- Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S., Wilkins, M. R., & Appel, R. D., Bairoch, A. (2005). Protein identification and analysis tools on the ExPASy server. In John M. Walker (Ed.), The proteomics protocols handbook (pp. 560–571). Humana Press.
- Gernez, Y., de Jesus, A. A., Alsaleem, H., Macaubas, C., Roy, A., Lovell, D., Jagadeesh, K. A., Alehashemi, S., Erdman, L., Grimley, M., Talarico, S., Bacchetta, R., Lewis, D. B., Canna, S. W., Laxer, R. M., Mellins, E. D., Goldbach-Mansky, R., & Weinacht, K. G. (2019). Severe autoinflammation in 4 patients with C-terminal variants in cell division control protein 42 homolog (CDC42) successfully treated with IL-1β inhibition. J. Allergy Clin. Immunol, 144(4), 1122–1125. https://doi.org/https://doi.org/10.1016/j.jaci.2019.06.017
- Guex, N., Peitsch, M. C., & Schwede, T. (2009). Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: A historical perspective. Electrophoresis, 30(S1), S162–S173. https://doi.org/https://doi.org/10.1002/elps.200900140
- Hassan, M., Abbas, Q., Raza, H., Moustafa, A. A., & Seo, S. Y. (2017). Computational analysis of histidine mutations on the structural stability of human tyrosinases leading to albinism insurgence. Molecular Biosystems, 13(8), 1534–1544. https://doi.org/https://doi.org/10.1039/c7mb00211d
- Heanue, T. A., Davis, R. J., Rowitch, D. H., Kispert, A., McMahon, A. P., Mardon, G., & Tabin, C. J. (2002). Dach1, a vertebrate homologue of drosophila dachshund, is expressed in the developing eye and ear of both chick and mouse and is regulated independently of Pax and Eya genes. Mechanisms of Development, 111(1–2), 75–87. https://doi.org/https://doi.org/10.1016/s0925-4773(01)00611-6
- Hu, C. Y., Mohtat, D., Yu, Y., Ko, Y.-A., Shenoy, N., Bhattacharya, S., Izquierdo, M. C., Park, A. S. D., Giricz, O., Vallumsetla, N., Gundabolu, K., Ware, K., Bhagat, T. D., Suzuki, M., Pullman, J., Liu, X. S., Greally, J. M., Susztak, K., & Verma, A. (2014). Kidney cancer is characterized by aberrant methylation of tissue-specific enhancers that are prognostic for overall survival. Clinical Cancer Research: An Official Journal of the American Association for Cancer Research, 20(16), 4349–4360. PMC][https://doi.org/10.1158/1078-0432.CCR-14-0494]
- Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics., 14(1), 33–38. https://doi.org/https://doi.org/10.1016/0263-7855(96)00018-5
- Ikeda, K., Watanabe, Y., Sno, H., Ohto, I., & Kawakami, K. (2002). Molecular interaction and synergistic activation of a promoter by Six, Eya, and Dach proteins mediated through CREB binding protein. Molecular and Cellular Biology, 22(19), 6759–6766. https://doi.org/https://doi.org/10.1128/MCB.22.19.6759-6766.2002
- Jayaraj, J. M., Krishnasamy, G., Lee, J. K., & Muthusamy, K. (2019). In silico identification and screening of CYP24A1 inhibitors: 3D QSAR pharmacophore mapping and molecular dynamics analysis. Journal of Biomolecular Structure and Dynamics, 37(7), 1700–1714. https://doi.org/https://doi.org/10.1080/07391102.2018.1464958
- Jayaraj, J. M., Reteti, E., Kesavan, C., & Muthusamy, K. (2020). Structural insights on vitamin D receptor and screening of new potent agonist molecules: Structure and ligand-based approach. Journal of Biomolecular Structure and Dynamics, 11, 1–12. https://doi.org/https://doi.org/10.1080/07391102.2020.1775122
- Kim, M. L., Chae, J. J., Park, Y. H., Nardo, D. D., Stirzaker, R. A., Ko, H. Y., Tye, H., Cengia, L., DiRago, L., Metcalf, D., Roberts, A. D., Kastner, D. L., Lew, A. M., Lyras, D., Kile, B. T., Croker, B. A., & Masters, S. L. (2015). Aberrant actin depolymerization triggers the pyrin inflammasome and autoinflammatory disease that is dependent on IL-18, not IL-1beta. Journal of Experimental Medicine, 212(6), 927–938. https://doi.org/https://doi.org/10.1084/jem.20142384
- Lakshmanan, L., Muthusamy, K., Marshal, J. J., Kajamaideen, A., & Balthasar, J. J. (2019). In silico insights on Tankyrase protein: A potential target for colorectal cancer. Journal of Biomolecular Structure & Dynamics, 37(14), 3637–3648. https://doi.org/https://doi.org/10.1080/07391102.2018.1521748
- Larsson, A. (2014). AliView: A fast and lightweight alignment viewer and editor for large datasets. Bioinformatics (Oxford, England), 30(22), 3276–3278. https://doi.org/https://doi.org/10.1093/bioinformatics/btu531
- Liu, J., Li, M., Song, B., Jia, C., Zhang, L., Bai, X., & Hu, W. (2013). Metformin inhibits renal cell carcinoma in vitro and in vivo xenograft. Urologic Oncology, 31(2), 264–270. https://doi.org/https://doi.org/10.1016/j.urolonc.2011.01.003
- Mathew, B., Haridas, A., Ucar, G., Baysal, I., Adeniyi, A. A., Soliman, M. E., Joy, M., Mathew, G. E., Lakshmanan, B., & Jayaprakash, V. (2016). Exploration of chlorinated thienyl chalcones: A new class of monoamine oxidase-B inhibitors. International Journal of Biological Macromolecules, 91, 680–695. https://doi.org/https://doi.org/10.1016/j.ijbiomac.2016.05.110
- Mishra, S. K., Mazumdar, A., Vadlamudi, R. K., Li, F., Wang, R. A., Yu, W., Jordan, V. C., Santen, R. J., & Kumar, R. (2003). MICoA, a novel metastasis-associated protein 1 (MTA1) interacting protein coactivator, regulates estrogen receptor-alpha transactivation functions. Journal of Biological Chemistry, 278(21), 19209–19219. https://doi.org/https://doi.org/10.1074/jbc.M301968200
- Miyake, M., Goodison, S., Lawton, A., Zhang, G., Gomes-Giacoia, E., & Rosser, C. J. (2013). Erythropoietin is a JAK2 and ERK1/2 effector that can promote renal tumor cell proliferation under hypoxic conditions. Journal of Hematology & Oncology, 6, 65. https://doi.org/https://doi.org/10.1186/1756-8722-6-65
- Molecular Operating Environment (MOE). 2016. Chemical Computing Group Inc., Montreal, QC, Canada. http://www.chemcomp.com/MOEMolecular_Operating_Environment.htm
- Mor, A., & Philips, M. R. (2006). Compartmentalized Ras/MAPK signaling. Annual Review of Immunology, 24, 771–800. https://doi.org/https://doi.org/10.1146/annurev.immunol.24.021605.090723
- Özgeriş, B., Göksu, S., Polat Köse, L., Gülçin, İ., Salmas, R. E., Durdagi, S., Tümer, F., & Supuran, C. T. (2016). Acetylcholinesterase and carbonic anhydrase inhibitory properties of novel urea and sulfamide derivatives incorporating dopaminergic 2-aminotetralin scaffolds. Bioorganic & Medicinal Chemistry, 24(10), 2318–2329. https://doi.org/https://doi.org/10.1016/j.bmc.2016.04.002
- Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera-a visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/https://doi.org/10.1002/jcc.20084
- Popov, V. M., Wu, K., Zhou, J., Powell, M. J., Mardon, G., Wang, C., & Pestell, R. G. (2010). The dachshund gene in development and hormone-responsive tumorigenesis. Trends in Endocrinology and Metabolism: TEM, 21(1), 41–49. https://doi.org/https://doi.org/10.1016/j.tem.2009.08.002
- Powe, D. G., Dhondalay, G. K., Lemetre, C., Allen, T., Habashy, H. O., Ellis, I. O., Rees, R., & Ball, G. R. (2014). DACH1: Its role as a classifier of long term good prognosis in luminal breast cancer. PLoS One., 9(1), e84428. https://doi.org/https://doi.org/10.1371/journal.pone.0084428
- Studio, D. (2008). Discovery, version 2.1. Accelrys.
- Turner, P. (2005). XMGRACE, version 5.1. 19.Center for coastal and land-margin research. Oregon Graduate Institute of Science and Technology.
- Wiederstein, M., & Sippl, M. J. (2007). ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research, 35, 407–410.
- Willard, L., Ranjan, A., Zhang, H., Monzavi, H., Boyko, R. F., Sykes, B. D., & Wishart, D. S. (2003). VADAR: A web server for quantitative evaluation of protein structure quality. Nucleic Acids Research, 31(13), 3316–3319. https://doi.org/https://doi.org/10.1093/nar/gkg565
- Wong, C. W., McNally, C., Nickbarg, E., Komm, B. S., & Cheskis, B. J. (2002). Estrogen receptor-interacting protein that modulates its nongenomic activity-crosstalk with Src/Erk phosphorylation cascade. Proceedings of the National Academy of Sciences of the United States of America, 99(23), 14783–14788. https://doi.org/https://doi.org/10.1073/pnas.192569699
- Wu, K., Chen, K., Wang, C., Jiao, X., Wang, L., Zhou, J., Wang, J., Li, Z., Addya, S., Sorensen, P. H., Lisanti, M. P., Quong, A., Ertel, A., & Pestell, R. G. (2014). Cell fate factor DACH1 represses YB-1-mediated oncogenic transcription and translation. Cancer Research, 74(3), 829–839. https://doi.org/https://doi.org/10.1158/0008-5472.CAN-13-2466
- Wu, K., Katiyar, S., Witkiewicz, A., Li, A., McCue, P., Song, L. N., Tian, L., Jin, M., & Pestell, R. G. (2009). The cell fate determination factor dachshund inhibits androgen receptor signaling and prostate cancer cellular growth. Cancer Research, 69(8), 3347–3355. https://doi.org/https://doi.org/10.1158/0008-5472.CAN-08-3821
- Wu, K., Li, A., Rao, M., Liu, M., Dailey, V., Yang, Y., Di Vizio, D., Wang, C., Lisanti, M. P., Sauter, G., Russell, R. G., Cvekl, A., & Pestell, R. G. (2006). DACH1 is a cell fate determination factor that inhibits Cyclin D1 and breast tumor growth. Molecular and Cellular Biology, 26(19), 7116–7129. https://doi.org/https://doi.org/10.1128/MCB.00268-06
- Wu, K., Li, Z., Cai, S., Tian, L., Chen, K., Wang, J., Hu, J., Sun, Y., Li, X., Ertel, A., & Pestell, R. G. (2013). EYA1 phosphatase function is essential to drive breast cancer cell proliferation through cyclin D1. Cancer Research, 73(14), 4488–4499. https://doi.org/https://doi.org/10.1158/0008-5472.CAN-12-4078
- Xiong, X., Huang, S., Zhang, H., Li, J., Shen, J., Xiong, J., Lin, Y., Jiang, L., Wang, X., & Liang, S. (2009). Enrichment and proteomic analysis of plasma membrane from rat dorsal root ganglions. Proteome Science, 7, 41https://doi.org/https://doi.org/10.1186/1477-5956-7-41
- Yan, W., Wu, K., Herman, J. G., Brock, M. V., Fuks, F., Yang, L., Zhu, H., Li, Y., Yang, Y., & Guo, M. (2013). Epigenetic regulation of DACH1, a novel Wnt signaling component in colorectal cancer. Epigenetics, 8(12), 1373–1383. https://doi.org/https://doi.org/10.4161/epi.26781
- Yan, W., Wu, K., Herman, J. G., Brock, M. V., Zhou, Y., Lu, Y., Zhang, Z., Yang, Y., & Guo, M. (2014). Epigenetic silencing of DACH1 induces the invasion and metastasis of gastric cancer by activating TGF-β signalling. Journal of Cellular and Molecular Medicine, 18(12), 2499–2511. https://doi.org/https://doi.org/10.1111/jcmm.12325
- Young, S. G., Ambroziak, P., Kim, E., & Clarke, S. (2001). Postisoprenylation protein processing: CXXX (CaaX) endoproteases and isoprenylcysteine carboxyl methyltransferase. In F. Tamanoi & D. S. Sigman (Eds.), The Enzymes (pp. 155–213). Academic Press.
- Zhang, J., Ren, X., Wang, B., Cao, J., Tian, L., & Liu, M. (2018). Effect of DACH1 on proliferation and invasion of laryngeal squamous cell carcinoma. Head Face Med, 14(1), 20https://doi.org/https://doi.org/10.1186/s13005-018-0177-1
- Zhu, H., Wu, K., Yan, W., Hu, L., Yuan, J., Dong, Y., Li, Y., Jing, K., Yang, Y., & Guo, M. (2013). Epigenetic silencing of DACH1 induces loss of transforming growth factor-β1 antiproliferative response in human hepatocellular carcinoma. Hepatology (Baltimore, Md.), 58(6), 2012–2022. https://doi.org/https://doi.org/10.1002/hep.26587